


Secret Life of a Secret Agent

by jessicacosta528



Series: The Makings of a Family [2]
Category: Bones (TV), NCIS
Genre: Family, Hurt/Comfort, M/M, Mpreg, Romance
Language: English
Status: In-Progress
Published: 2012-10-27
Updated: 2012-11-10
Packaged: 2017-11-17 04:24:54
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 4
Words: 4,735
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/547580
Author URL: https://archiveofourown.org/users/jessicacosta528/pseuds/jessicacosta528
Summary: <blockquote class="userstuff">
              <p>continuation of Life is Good. should read that first to get references. What happens when something goes wrong for Tony what choices does he have to make? and what confrontations come out of those decisions? is his secret almost out? Slash and implied Mpreg. if you dont like that then dont read. Review</p>
            </blockquote>





	1. Chapter 1

Secret Life of a Special Agent  
A/N: So this is my second NCIS/Bones crossover fanfic. This is the second to my Life is good story. It doesn’t begin in the beginning it’s just a continuation one. I am still working on a prequel for Life is good. I’m just having writers block for that one. Constructive criticism would be greatly appreciated. This story is AU and may not follow much from the story just so you know. But anyway on to the story, I hope you enjoy!

Disclaimer: I wish I did but sadly I do not own these amazing characters. But if I did I would have them come together in the show, have Tony and Booth together with kids and everything else my way.

Sitting behind a desk all day doing cold cases was not Tony’s idea of fun. Not that he wanted anyone to die or anything, he just hated not having a case.

All he could think about was his husband at work and his three kids at day care. His kids had grown up so quickly it was crazy. Jason and Jasper were already in their not-so-terrible-twos. They were good kids and always behaved but you had to always keep an eye on them. They were so mischievous and got into everything. His youngest, a bright little boy, Travis Bradley had just turned one year old. Trav had just started going to day care when before he would stay with his Uncle Steve and Aunt Jenna, who were long time friends with Tony.

No one at NCIS, or the FBI for that matter, knew he had a husband or kids. It isn’t like he didn’t want people to know or was ashamed of them of them he just liked to have his private life. It wasn’t that hard to keep people away from certain topic. Tony just talked about his heterosexual love life that was nonexistent but no one ever questioned it. 

Everyone thought he was a womanizing frat boy and he never tried to convince them they were wrong. He believed it was safer for his family by keeping his work life and personal life separately. 

The ringing of Tony’s phone brought everyone out of their concentration on their work.

“Hello, Very Special Agent Anthony DiNozzo speaking. How may I help you?” he said as nicely as he could causing Ziva and McGee to roll their eyes and Gibbs to continue with his work.

The smile dropped off of Tony’s face only to be replaced with a frown. “How?... No if he’s busy don’t bother him… Yea I’m sure… Okay see you soon.”

Looking over at Gibbs Tony got up and was packing his things. He then grabbed his gun to put it in the holster and put his badge in his pocket. “Boss, I need to leave now.”

“What do you need to leave for?” Gibbs practically growled.

“Family emergency,” Tony said.

“I thought you didn’t have any family?” Ziva said with conviction.

“Yea didn’t you say you didn’t have any?” McGee added.

“Yes teams do not keep secrets from each other,” Ziva expressed.

“Right like you two don’t keep secrets. Like you shared about Rivkin and McGee like you shared about your sister possibly being a murder suspect! Yea real team sharing there.” Tony practically yelled and turned back to Gibbs, “Well can I go?”

“Who in your family do you have to see?” Gibbs asked.

Tony sighed, “Does it matter who? Shouldn’t it only matter that it’s a family emergency?”

“I think he is lying if he does not want to tell you who the “emergency” is about.” Ziva said with the usual air of arrogance she always had when she thought she was right. McGee nodded in agreement.

“You know what, fine I’m leaving I don’t care. I need to be somewhere right now and I don’t have to put up with this unprofessional and harassing treatment.” With that Tony stormed to the elevator and disappeared. 

“What was wrong with him? Can he not take it?” Ziva asked even though she knew the answer but just didn’t care.

Everything in the squad went back to normal. Gibbs didn’t like how his team was treating Tony or how Tony had a secret. He couldn’t get the family emergency out of his head. He would stop by Tony’s later maybe he’ll get to the bottom of it. No he will get to the bottom of it.


	2. Chapter 2

**Summary for the Chapter:**

> continuation of Life is Good. should read that first to get references. What happens when something goes wrong for Tony what choices does he have to make? and what confrontations come out of those decisions? is his secret almost out? Slash and implied Mpreg. if you dont like that then dont read. Review! Chapter 2 now up

Secret Life of a Special Agent  
A/N: So this is my second NCIS/Bones crossover fanfic. This is the second to my Life is good story. It doesn’t begin in the beginning it’s just a continuation one. I am still working on a prequel for Life is good. I’m just having writers block for that one. Constructive criticism would be greatly appreciated. This story is AU and may not follow much from the story just so you know. But anyway on to the story, I hope you enjoy! So just remember Tony is 31 and Seeley is 32. Tony was 20 and Seeley was 21 when they got married.

Disclaimer: I wish I did but sadly I do not own these amazing characters. But if I did I would have them come together in the show, have Tony and Booth together with kids and everything else my way.

Arriving home Tony turned off the vehicle and rested his head on the steering wheel. He couldn’t believe he blew up like that in the bullpen. Of course it was justifiable but still he shouldn’t have. Looking in to the rear view mirror brought a smile to his face, there sleeping in the back were his three amazing boys.

He had had to stop at the day care to pick up a sick Travis. So instead of having to make two trips he just picked up Jason and Jasper too. Seeley couldn’t be reached probably due to a case. He sometimes wishes Seeley didn’t have to work so much and had time for him and the kids. He wasn’t complaining though, he knew what the job was like. 

Finally getting out of the truck Tony moved to the other side and opened the back door. Pulling out the double stroller from the back, Tony placed both sleeping two year olds, Jason and Jasper, into the seats and strapped them in. He then pulled Trav and carried him while pushing the stroller up to the house. He soon had the front door locked and moved to the twins’ room. Gently placing both into their own cribs, Tony gave them both a kiss on their foreheads. He then moved to Travis’ room to change and clothe him for bed. Soon he was asleep in his crib.

Moving to his bedroom he turned both baby monitors on and changed into sweats and a long sleeve t-shirt. Feeling drained and exhausted Tony curled into bed and was soon pulled into a restful and dreamless sleep.

The house was silent as he entered the front door. Work had ended fairly early so Seeley was able to leave that much sooner. He listened to his voicemails about Travis being sick and felt guilty because Tony was stuck doing everything by him self like usual.

Opening the twins’ door Seeley peaked in to see they were still asleep. He smiled affectionately at his first born sons and gave them each kisses on their sandy brown locks on their little heads. He moved to Travis’ room.

As he opened the door he saw Travis staring at him with Tony’s intense eyes that seemed more mature than they were. His little cheeks were flushed with fever and he looked every bit as sick as he was. 

“What Baby Boy, couldn’t sleep?” Seeley whispered as he made his way to pick Travis up. Walking him around usually helped him go back to sleep. Just as he was leaving Travis’ room he heard the doorbell. 

“Huh, I wonder who that could be, huh Trav?” Seeley asked as he pulled Travis closer to him. 

Opening the door Seeley recognized the man by the stories he was told, “Can I help you?”

Seeley saw the curious look pointed at him then Travis. But when Travis looked at Gibbs, Gibbs’ brows furrowed.

“Who is the boy? Is he related to Tony?” Gibbs asked noticing the boy had the same eyes as Tony’s.

“Well yea I would thing he was related to his son,” Seeley said being slightly sarcastic but with a smile. 

The look on Gibbs’ face was priceless, he looked about to have a conniption. “Tony has a son?” his tone was one of incredulousness.

“Yes, he has three. This is just the youngest.”

“Who is the other parent? And who are you?”

“Well first I am and I am their father and Tony’s husband for eleven years.”

“How come he never talks about you then?”

“It’s safer that way. You know with jobs like ours it’s not safe with people knowing you have a family when they can use that against you for revenge.” 

Gibbs just nodded.

Travis began to squirm and looked like he was going to start crying.

“Do you want to come in? I need to give Trav some medicine.”

“Sure,” Gibbs answered following Booth in.

“Sorry about before I was just curious as to why you were here. I’m Seeley Booth,” he offered along with his hand extended out towards Gibbs.

“Jethro Gibbs, Tony’s boss but you probably already knew that.” Gibbs reciprocated the handshake.

Seeley turned around and opened the fridge. Grabbing out the medicine Booth measured out the amount and put it into a syringe. Gently he placed the syringe into Travis’ mouth and pressed down the pump sending the medicine into his mouth.

Travis didn’t look too happy with the taste and got red faced. He began to tear up and soon busted out crying.

“Oh come on Baby Boy. There is no need for that now. It’s just medicine to make you feel better. Come on shhh. Booth continued to bop Travis gently up and down and say reassuring things into his silky brown wavy locks with kisses.

Gibbs’ heart constricted just thinking about doing the same thing for Kelly as a baby.

The crying seemed to attract someone, hearing a door open Seeley looked up.

“Hey sorry to wake you up, Trav just needed his meds.” Booth said lightly when he spotted his husband in sweats and his dark grey FBI long sleeve t-shirt. 

Smiling lightly Tony shook his head, “its okay I just heard my Baby Boy crying,” Tony said grabbing Travis from Seeley. When Travis got into Tony’s arms he suddenly stopped crying and was soon asleep. 

“I still have no idea how you do that,” Booth said trying to look mad but failed when the corner of his mouth went up.

“I’m just amazing what can I say?” Tony asked laughing. Giving Booth a kiss Tony was about to deepen it when he heard some one clearing their throat.

Startled Tony turned around and held Travis closer to his body.

“Boss?!” Tony squeaked not at all anticipating the turn of events.

TBC


	3. Finding out

**Summary for the Chapter:**

> What happens when Gibbs finds out about Tony's family? what things will be revealed and how will it change everyone's lives that are involved?

Secret Life of a Special Agent  
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“I’m just amazing what can I say?” Tony asked laughing. Giving Booth a kiss Tony was about to deepen it when he heard some one clearing their throat.

Startled Tony turned around and held Travis closer to his body.

“Boss?!” Tony squeaked not at all anticipating the turn of events.

҉҉҉҉

“Boss what are you doing here?” Tony was trying his best not to look nervous. He looked between Booth and Gibbs, looking for an explanation.

“I wanted to make sure that the emergency was okay and to say that that attitude in the bullpen towards you will not happen again.”

Knowing that was the closest thing he would get of an apology Tony smiles, “Thanks Boss. Um yea the emergency is getting there. Travis here was sick and I was the only one who could go and get him.”

“Well that’s good. He’s an adorable kid,” Gibbs said with a smile as he looked at Travis who looked like a mini version of Tony. They had the same eyes and the same soft looking strands of chestnut brown hair. Gibbs could imagine they would have the same smile too if Travis wasn’t sick. There was almost no part of Booth in the boy’s features.

“Thanks,” Tony and Booth both spoke at the same time bringing a smile to both of their faces. “Boss, would you like some coffee or something?”

“Sure, I could definitely go for some coffee.”

Booth then excused himself from the room, to check on the twins, taking a sleeping Travis with him to put him in his room.

Gibbs observed Tony as he was working on the coffee; he didn’t look or act any different. How could he have missed that Tony had a family: a husband to begin with and three kids. ‘So much for being a good investigator’ Gibbs thought grudgingly to himself.

“Nobody really knows about my other life Boss,” Tony spoke up bringing Gibbs out of his thoughts. “Not even Seeley’s colleagues know about us or the kids.” Tony had turned around to look at Gibbs.

Gibbs could only nod. Looking around the house Gibbs felt the house had a lot of love in it and had a lived in feel to it. There were toys neatly pilled into a toy box in the corner, baby blankets folded on the side of the couch, 2 playpens towards the back wall and a few stuffed animals and toys in each. He had always believed that Tony could have the best of both worlds: the job he loved and a family. Only now he realized Tony already had both and seemed happy with it. He had always thought he had had a chance to give that life to Tony, but sitting here in Tony and another man’s kitchen, observing things that belonged to their children, Gibbs knew not to try anything no matter how much he wanted to. Just wrap Tony up in his arms, kiss him senseless and beg him to run away with him and the kids. It was a long shot he knew that’s why it was only a thought and not turned into an action.

“Boss, can you not tell anyone about this, we’re trying to keep it quiet? You never know what someone would try to use against you and I really can’t lose my kids, I just don’t know what I would do.” 

“It’s not a problem; this can just stay between you and me. I wouldn’t ruin your trust by saying anything that is not anyone’s business but yours. And I wouldn’t want anything to happen to your kids because I couldn’t keep my mouth shut.”

“Thank you Gibbs.” Tony gave him a grateful smile then turned around and poured the coffee into a cup that said FBI on it and handed it to Gibbs. Tony had to laugh at the face Gibbs made when he was handed the cup. 

“Oh just drink it. I promise I won’t tell anyone about it.”

“Good you better not.” Grinned Gibbs and added, “I have a reputation to uphold.” Tony barked out a laugh at that.

The sound of pitter pattering feet made them both look up just in time to see two blurs to launch themselves at Tony, who scooped them up readily like they did this many times before. Tony then proceeded to blow raspberries on their tummies drawing high pitched but adorable giggles from them both bringing a smile to Tony and Gibbs’ faces. 

“Daddy! Daddy stop!” They both yelled breathlessly in unison from the continuous laughing. 

Laughing Tony stopped his actions, “Okay, okay. So how were your naps?”

“Good Daddy, we sleeped really long!” Jason spoke up while Jasper continued to nod his head vigorously. They both held onto Tony tight and gave him sloppy kisses to his cheeks, which only made his smile bigger.

“Okay boys you can meet my boss, this is Gibbs. What do you say?”

“Hi Boss,” Jason said while waving his little hand. “Nice to meet you,” Jasper added with his own wave.

“Hi boys, what are your names?” Gibbs couldn’t suppress his smile with Tony’s two adorable twin sons. 

“He’s Jasper and I’m Jason.” Jason proceeded to point them both out while talking. Jason was always the more forward of the two while Jasper was the more quiet one.

“Well hello Jason and Jasper.” Gibbs then turned to Tony and added, “How old are they?”

“They’re two years old and tuning closer to three everyday.” Tony’s whole face lit up when he talked about his precious children.

“I know how that goes. They grow up so quick it seems the time flies away.” Gibbs’ eyes got that far away look they usually got when he thought about Shannon and Kelly. He mentally shook himself to keep the topics light. 

Tony gave him a sad but knowing smile and nodded, “Yea that is does.” He then looked to his sons in his arms and gave them both kisses on their dark locks. “Why don’t you guys quietly go play in the living room, okay?” As they were about to run away Tony added, “Play quietly! You know your brother needs his sleep.”

“Yes Daddy!” Said the excited two year olds in unison.

Gibbs just laughed and shook his head. As he looked at Tony watching his boys play he deduced that fatherhood was a very good look on Tony. ‘If I had only acted sooner this could be my life with Tony watching our children play,’ kept going through his head ‘yea right it would have had to be around eleven years before.’

Seeley then walked into the kitchen again and put an arm around Tony’s waist and kissed his head before going over to the coffee machine. As he was making himself a cup he followed the others’ gazes and it landed on his sons playing. It brought a knot to his stomach thinking about his happy family and what his mistake could do to it.

Soon Gibbs had to leave and was walked out by Tony, which is how he found himself now sitting in his car thinking about things. Thinking about all the mistakes he had made and all of the chances he missed because he was too stubborn. He vowed to himself if he got the chance to have everything he wanted he would not hesitate to take it. 

Finally sighing Gibbs looked at the house one more time and drove to his empty and forlorn house and hoped that morning would come soon to end the lonely night. 

TBC… Soon


	4. The end or the beginning?

Secret Life of a Special Agent  
**§**  
Seeley then walked into the kitchen again and put an arm around Tony’s waist and kissed his head before going over to the coffee machine. As he was making himself a cup he followed the others’ gazes and it landed on his sons playing. It brought a knot to his stomach thinking about his happy family and what his mistake could do to it.

Soon Gibbs had to leave and was walked out by Tony, which is how he found himself now sitting in his car thinking about things. Thinking about all the mistakes he had made and all of the chances he missed because he was too stubborn. He vowed to himself if he got the chance to have everything he wanted he would not hesitate to take it. 

Finally sighing Gibbs looked at the house one more time and drove to his empty and forlorn house and hoped that morning would come soon to end the lonely night.   
**§**

Gibbs had just started working on the boat when he heard the knocking. No one had knocked on his front door that knew him because he always left it unlocked. But who would be at his house at this hour?

When he finally made it upstairs he was shocked as he pulled open the door. Standing there was Tony and his boys.

From observing Tony he could tell that he had been crying recently. His twins were both asleep in the double stroller while Travis was asleep in his arms. A diaper bag was slung over his left shoulder.

“Come in Tony, you didn’t have to wait outside or knock. Here let me take the twins and your bag.” Tony only nodded as he handed over the bag and stroller. Gibbs then ushered him inside the house into the seldom used living room.

“Why don’t we put these guys down in the guest room? There’s plenty of room.” Once again he was only met with a silent nod.

Gibbs unstrapped the stroller’s straps and grabbed each twin up into his arms. They both snuggled deeper into his arms and Jasper started sucking on his thumb which brought a smile to Gibbs’ face.

When they reached the guestroom Gibbs laid the twins on the full sized bed and put pillows around them so they wouldn’t fall on the ground by rolling around. Gibbs took the baby monitor, which Tony packed, out of the diaper bag and turned it on. He put the side lamp on as a night light and quietly left the room. He then walked over to a room Tony had never seen open and soon came back with a beautiful crib.

Tony startled at seeing the crib. “Gibbs you don’t need to bring that out. I can have Travis sleep with me on the couch, its fine.”

Gibbs only ignored him and walked over to the master bedroom and put the crib close to the bed. He then took a sleeping Travis from Tony and placed him in the crib gently and placed a blanket on his small form. Luckily there was two baby monitors packed so each room could have one. Switching the lamp on Gibbs left the room with Tony following close behind.

“So are you going to tell me what happened?” Gibbs asked softly.

“Um… Seeley and I… had a fight. And um I don’t see it ever getting better. It’s over between us for good. I didn’t know where else to go so I came here. Being in the house was just too much for me.” Tony had tears rolling down his cheeks as he remembered everything that happened.

“What was the fight about?” Gibbs was angry at the FBI agent for making Tony ever cry. Tony then began to tell Gibbs what happened.

**§Flashback§**

After he had put the kids to bed, Tony made his way upstairs to Seeley and his bedroom. As he entered the room he saw Seeley just standing there not really looking at anything in particular. It was odd for him to just stand around, he always seemed to be doing something and always being on the move. 

Tony walked over and gave Seeley a hug. What shocked Tony was at first Booth stiffened and finally returned the hug. Looking up at Booth, Tony saw something in Booth’s face that worried him.

“Hey what’s wrong?” Tony asked not understanding what was wrong.

As Seeley looked down at Tony he finally found his voice, “We need to talk.”

Tony’s stomach went into a knot as he was led over to the bed where they both sat down and faced each other. Booth took his hand between his.

“Remember when that guy I worked with died and I had stayed at the apartment I keep, to keep up appearances for work? Well I… I wasn’t alone. My colleague Temperance “Bones” was there too. And later she was crying so I told her to lay with me.” By then Tony’s stomach had dropped, making him feel sick. But Seeley kept going, “And it just happened and we slept together. But she told me that she’s… um she’s pregnant, with my baby.” Tony pulled his hand away and just sat there. His throat began to feel full like it always did when he was close to tears.

“Say something, anything.” Booth broke the silence. 

“Get out, now. You can’t stay here anymore.” Tony spoke in a quiet but stern voice that spoke volumes about how he was feeling. Looking into Seeley’s eyes Tony added, “I want a divorce and I’m taking the kids. Now get out of my house, now.”

Seeley nodded and before he left he looked back and saw Tony in the same spot. He had never seen Tony like this before and he hated himself for being the one to do this to Tony. ‘How could you be such an idiot Booth?’

The sound of the door being shut reverberated in Tony’s head signaling the end to his eleven year love. He knew that everything was done between them. He would never put up what his mom had with his father even though it was never to the same extent. 

Tony couldn’t hold his emotions in any longer, he curled up in on himself and cried. He cried for the love that was lost, for the man he believed his husband was, for his kids who would be put in the middle of everything and for himself. He had to learn to live independently again and as a single parent.

He finally stopped crying. No he would stop feeling sorry for himself; he didn’t need Booth to care for him or the boys. He had been doing everything for the boys and Booth had only been there occasionally. 

Being in the house that had been theirs for longer than five years though was too much on him right now. Even though Seeley was not there at the moment there were memories all throughout the house at every turn. He feared if he didn’t leave soon he would take Seeley back and end up as one of the people who always went back after all of the mistakes their others did. 

He packed up the kids with everything they needed and put them in the truck. He drove to the only place he could think of, the only place he felt safe; Gibbs’ house. 

**§End Flashback§**

Gibbs was shocked he would have never guessed that that was what happened. He looked over to Tony and saw him crying so he pulled him into a tight hug. 

That seemed to loosen something in Tony because a dam seemed to have been broken and all of Tony’s emotions poured out. 

Gibbs continued to run his fingers through the soft chestnut strands of hair that were softer than he thought. A little under ten minutes ago Tony’s breath had evened out signaling he had finally gotten to sleep.

Gibbs didn’t want to wake Tony but sleeping like this would end in a very sore day tomorrow so Gibbs gently prodded Tony awake. 

“Come on Tony you have to get up, you should move to the upstairs bedroom.”

Tony’s reply was to mumble and snuggle into Gibbs’ chest more. Gibbs really liked the feeling of having a warm body in his arms again but the best part of it is that it was Tony; the man he had loved for years.

“Okay fine, but I’m only doing this once.” Gibbs then grabbed Tony and picked up. He was lighter than Gibbs once believed. 

When he mad it to the master bedroom Gibbs placed Tony down and pulled the covers up over him.

As he was walking away Tony seemed to have another idea. Gibbs found himself on top of the bed with Tony cuddled up next to him. Tony’s hand had the front of his shirt in a death grip and his head on Gibbs’ chest. Gibbs’ knew he should stop this but he loved the feeling of Tony in his arms and having Tony’s kids in the same house. He would protect Tony and Tony’s boys with everything he had even from one Seeley Booth.

He was soon hypnotized by the sounds of four sets of even breathing that he was soon pulled into a restful sleep. 

TBC: Soon. I love reviews so please leave them! Also I know where the story is going so it will be updated hopefully soon. Everything will be answered later for anyone who has questions about the story.


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